Abstract
The potentials of mean force (PMFs) dependent on orientation were determined for system involving formation of hydrophobic dimer composed of modelling side chain—side chain interaction in water, using the TIP3P water model. A series of umbrella‐sampling molecular dynamics simulations with the AMBER force field was carried out for a system modelling side chain—side chain interactions of a pair Val‐Phe, in water. The PMFs dependent on orientation were calculated by using the Weighted Histogram Analysis Method (WHAM). The shape of PMFs for the dimer dependent on side‐chain orientation is characteristic for hydrophobic interactions with contact and solvent‐separated minima, and desolvation maxima. The position of all these minima and maxima change with the distance between centres of interactions.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
